#1146: Additional fixes for Medication-related resource retrieves

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/Cql2ElmVisitor.java

@@ -2919,16 +2919,19 @@ public Expression visitRetrieve(cqlParser.RetrieveContext ctx) {
                 if (hasFHIRHelpers
                         && propertyType instanceof NamedType
                         && ((NamedType) propertyType).getSimpleName().equals("Reference")
-                        && namedType.getSimpleName().equals("MedicationRequest")) {
+                        && (namedType.getSimpleName().equals("MedicationRequest")
+                                || namedType.getSimpleName().equals("MedicationAdministration")
+                                || namedType.getSimpleName().equals("MedicationDispense")
+                                || namedType.getSimpleName().equals("MedicationStatement"))) {
                     // TODO: This is a model-specific special case to support QICore
                     // This functionality needs to be generalized to a retrieve mapping in the model
-                    // info
-                    // But that requires a model info change (to represent references, right now the
-                    // model info only
-                    // includes context relationships)
-                    // The reference expands to [MedicationRequest] MR with [Medication] M such that
-                    // M.id =
-                    // Last(Split(MR.medication.reference, '/')) and M.code in <valueset>
+                    // info. But that requires a model info change (to represent references, right
+                    // now the model info only includes context relationships)
+                    // The reference expands to
+                    //   [MedicationRequest] MR
+                    //     with [Medication] M
+                    //       such that M.id = Last(Split(MR.medication.reference, '/'))
+                    //         and M.code in <valueset>
                     Retrieve mrRetrieve = buildRetrieve(
                             ctx, useStrictRetrieveTyping, namedType, classType, null, null, null, null, null, null);
                     retrieves.add(mrRetrieve);
@@ -2939,7 +2942,7 @@ public Expression visitRetrieve(cqlParser.RetrieveContext ctx) {
                     Retrieve mRetrieve = buildRetrieve(
                             ctx, useStrictRetrieveTyping, mNamedType, mClassType, null, null, null, null, null, null);
                     retrieves.add(mRetrieve);
-                    mRetrieve.setResultType(new ListType((DataType) namedType));
+                    mRetrieve.setResultType(new ListType(mDataType));
                     Query q = of.createQuery();
                     AliasedQuerySource aqs = of.createAliasedQuerySource()
                             .withExpression(mrRetrieve)
@@ -2968,9 +2971,27 @@ public Expression visitRetrieve(cqlParser.RetrieveContext ctx) {
                     Equal e = of.createEqual().withOperand(idProperty, last);
                     libraryBuilder.resolveBinaryCall("System", "Equal", e);
 
+                    // Apply target mapping if this is a profile-informed model info
+                    if (DataTypes.equal(idType, libraryBuilder.resolveTypeName("System", "String"))) {
+                        idProperty.setPath("id.value");
+                    }
+                    if (DataTypes.equal(refType, libraryBuilder.resolveTypeName("System", "String"))) {
+                        refProperty.setPath("medication.reference.value");
+                    }
+
                     DataType mCodeType = libraryBuilder.resolvePath((DataType) mNamedType, "code");
-                    Property mProperty = of.createProperty().withPath("code");
-                    mProperty.setResultType(mCodeType);
+                    Property mProperty = libraryBuilder.buildProperty("M", "code", false, mCodeType);
+                    Expression mCodeProperty = mProperty;
+
+                    // Apply target mapping if this is a profile-informed model info
+                    if (DataTypes.equal(mCodeType, libraryBuilder.resolveTypeName("System", "Concept"))) {
+                        FunctionRef toConcept = of.createFunctionRef()
+                                .withLibraryName("FHIRHelpers")
+                                .withName("ToConcept")
+                                .withOperand(mCodeProperty);
+                        toConcept.setResultType(mCodeType);
+                        mCodeProperty = toConcept;
+                    }
                     String mCodeComparator = "~";
                     if (terminology.getResultType() instanceof ListType) {
                         mCodeComparator = "in";
@@ -2985,9 +3006,9 @@ public Expression visitRetrieve(cqlParser.RetrieveContext ctx) {
 
                     Expression terminologyComparison = null;
                     if (mCodeComparator.equals("in")) {
-                        terminologyComparison = libraryBuilder.resolveIn(mProperty, terminology);
+                        terminologyComparison = libraryBuilder.resolveIn(mCodeProperty, terminology);
                     } else {
-                        BinaryExpression equivalent = of.createEquivalent().withOperand(mProperty, terminology);
+                        BinaryExpression equivalent = of.createEquivalent().withOperand(mCodeProperty, terminology);
                         libraryBuilder.resolveBinaryCall("System", "Equivalent", equivalent);
                         terminologyComparison = equivalent;
                     }

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/fhir/r401/BaseTest.java

@@ -3,6 +3,7 @@
 import static org.cqframework.cql.cql2elm.TestUtils.visitFile;
 import static org.cqframework.cql.cql2elm.TestUtils.visitFileLibrary;
 import static org.cqframework.cql.cql2elm.matchers.QuickDataType.quickDataType;
+import static org.hamcrest.CoreMatchers.notNullValue;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.*;
 
@@ -16,10 +17,7 @@
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.cqframework.cql.cql2elm.TestUtils;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
-import org.hl7.cql.model.ChoiceType;
-import org.hl7.cql.model.ClassType;
-import org.hl7.cql.model.DataType;
-import org.hl7.cql.model.NamespaceInfo;
+import org.hl7.cql.model.*;
 import org.hl7.elm.r1.*;
 import org.junit.jupiter.api.Test;
 
@@ -907,4 +905,105 @@ void overloadForwardOutput() throws IOException {
                         String.format(
                                 "You used a string literal: [Encounter] here that matches an identifier in scope: [Encounter]. Did you mean to use the identifier instead?")));
     }
+
+    @Test
+    void medicationRequest() throws IOException {
+        CqlTranslator translator = TestUtils.runSemanticTest("fhir/r401/TestMedicationRequest.cql", 0);
+        Library library = translator.toELM();
+        Map<String, ExpressionDef> defs = new HashMap<>();
+
+        if (library.getStatements() != null) {
+            for (ExpressionDef def : library.getStatements().getDef()) {
+                defs.put(def.getName(), def);
+            }
+        }
+
+        ExpressionDef def = defs.get("Antithrombotic Therapy at Discharge");
+        assertThat(def, notNullValue());
+        assertThat(def.getExpression(), instanceOf(Query.class));
+        Query q = (Query) def.getExpression();
+        assertThat(q.getSource().size(), is(1));
+        assertThat(q.getSource().get(0).getExpression(), instanceOf(Retrieve.class));
+        Retrieve r = (Retrieve) q.getSource().get(0).getExpression();
+        assertThat(r.getTemplateId(), is("http://hl7.org/fhir/StructureDefinition/MedicationRequest"));
+        assertThat(r.getCodeProperty(), is("medication"));
+        assertThat(r.getCodeComparator(), is("in"));
+        assertThat(r.getCodes(), instanceOf(ValueSetRef.class));
+        ValueSetRef vsr = (ValueSetRef) r.getCodes();
+        assertThat(vsr.getName(), is("Antithrombotic Therapy"));
+
+        def = defs.get("Antithrombotic Therapy at Discharge (2)");
+        assertThat(def, notNullValue());
+        assertThat(def.getExpression(), instanceOf(Union.class));
+        Union u = (Union) def.getExpression();
+        assertThat(u.getOperand().size(), is(2));
+        assertThat(u.getOperand().get(0), instanceOf(Retrieve.class));
+        r = (Retrieve) u.getOperand().get(0);
+        assertThat(r.getTemplateId(), is("http://hl7.org/fhir/StructureDefinition/MedicationRequest"));
+        assertThat(r.getCodeProperty(), is("medication"));
+        assertThat(r.getCodeComparator(), is("in"));
+        assertThat(r.getCodes(), instanceOf(ValueSetRef.class));
+        vsr = (ValueSetRef) r.getCodes();
+        assertThat(vsr.getName(), is("Antithrombotic Therapy"));
+
+        assertThat(u.getOperand().get(1), instanceOf(Query.class));
+        q = (Query) u.getOperand().get(1);
+        assertThat(q.getSource().size(), is(1));
+        assertThat(q.getSource().get(0).getExpression(), instanceOf(Retrieve.class));
+        r = (Retrieve) q.getSource().get(0).getExpression();
+        assertThat(r.getTemplateId(), is("http://hl7.org/fhir/StructureDefinition/MedicationRequest"));
+        assertThat(r.getCodeProperty() == null, is(true));
+        assertThat(r.getCodes() == null, is(true));
+        assertThat(q.getRelationship(), notNullValue());
+        assertThat(q.getRelationship().size(), is(1));
+        assertThat(q.getRelationship().get(0), instanceOf(With.class));
+        With w = (With) q.getRelationship().get(0);
+        assertThat(w.getExpression(), instanceOf(Retrieve.class));
+        r = (Retrieve) w.getExpression();
+        assertThat(r.getTemplateId(), is("http://hl7.org/fhir/StructureDefinition/Medication"));
+        assertThat(r.getCodeProperty() == null, is(true));
+        assertThat(r.getCodes() == null, is(true));
+        assertThat(r.getResultType(), instanceOf(ListType.class));
+        assertThat(((ListType) r.getResultType()).getElementType(), instanceOf(ClassType.class));
+        assertThat(((ClassType) ((ListType) r.getResultType()).getElementType()).getName(), is("FHIR.Medication"));
+        assertThat(w.getSuchThat(), instanceOf(And.class));
+        And a = (And) w.getSuchThat();
+        assertThat(a.getOperand().get(0), instanceOf(Equal.class));
+        Equal eq = (Equal) a.getOperand().get(0);
+        assertThat(eq.getOperand().get(0), instanceOf(FunctionRef.class));
+        FunctionRef fr = (FunctionRef) eq.getOperand().get(0);
+        assertThat(fr.getLibraryName(), is("FHIRHelpers"));
+        assertThat(fr.getName(), is("ToString"));
+        assertThat(fr.getOperand().size(), is(1));
+        assertThat(fr.getOperand().get(0), instanceOf(Property.class));
+        Property p = (Property) fr.getOperand().get(0);
+        assertThat(p.getScope(), is("M"));
+        assertThat(p.getPath(), is("id"));
+        assertThat(eq.getOperand().get(1), instanceOf(Last.class));
+        Last l = (Last) eq.getOperand().get(1);
+        assertThat(l.getSource(), instanceOf(Split.class));
+        Split s = (Split) l.getSource();
+        assertThat(s.getStringToSplit(), instanceOf(FunctionRef.class));
+        fr = (FunctionRef) s.getStringToSplit();
+        assertThat(fr.getLibraryName(), is("FHIRHelpers"));
+        assertThat(fr.getName(), is("ToString"));
+        assertThat(fr.getOperand().size(), is(1));
+        assertThat(fr.getOperand().get(0), instanceOf(Property.class));
+        p = (Property) fr.getOperand().get(0);
+        assertThat(p.getScope(), is("MR"));
+        assertThat(p.getPath(), is("medication.reference"));
+        // assertThat(s.getSeparator(), is("/"));
+        assertThat(a.getOperand().get(1), instanceOf(InValueSet.class));
+        InValueSet ivs = (InValueSet) a.getOperand().get(1);
+        assertThat(ivs.getValueset().getName(), is("Antithrombotic Therapy"));
+        assertThat(ivs.getCode(), instanceOf(FunctionRef.class));
+        fr = (FunctionRef) ivs.getCode();
+        assertThat(fr.getLibraryName(), is("FHIRHelpers"));
+        assertThat(fr.getName(), is("ToConcept"));
+        assertThat(fr.getOperand().size(), is(1));
+        assertThat(fr.getOperand().get(0), instanceOf(Property.class));
+        p = (Property) fr.getOperand().get(0);
+        assertThat(p.getScope(), is("M"));
+        assertThat(p.getPath(), is("code"));
+    }
 }

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/qicore/v411/BaseTest.java

@@ -13,6 +13,8 @@
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.cqframework.cql.cql2elm.TestUtils;
+import org.hl7.cql.model.ClassType;
+import org.hl7.cql.model.ListType;
 import org.hl7.elm.r1.*;
 import org.junit.jupiter.api.Test;
 
@@ -370,12 +372,38 @@ void medicationRequest() throws IOException {
         assertThat(r.getTemplateId(), is("http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medication"));
         assertThat(r.getCodeProperty() == null, is(true));
         assertThat(r.getCodes() == null, is(true));
+        assertThat(r.getResultType(), instanceOf(ListType.class));
+        assertThat(((ListType) r.getResultType()).getElementType(), instanceOf(ClassType.class));
+        assertThat(((ClassType) ((ListType) r.getResultType()).getElementType()).getName(), is("QICore.Medication"));
         assertThat(w.getSuchThat(), instanceOf(And.class));
         And a = (And) w.getSuchThat();
         assertThat(a.getOperand().get(0), instanceOf(Equal.class));
+        Equal eq = (Equal) a.getOperand().get(0);
+        assertThat(eq.getOperand().get(0), instanceOf(Property.class));
+        Property p = (Property) eq.getOperand().get(0);
+        assertThat(p.getScope(), is("M"));
+        assertThat(p.getPath(), is("id.value"));
+        assertThat(eq.getOperand().get(1), instanceOf(Last.class));
+        Last l = (Last) eq.getOperand().get(1);
+        assertThat(l.getSource(), instanceOf(Split.class));
+        Split s = (Split) l.getSource();
+        assertThat(s.getStringToSplit(), instanceOf(Property.class));
+        p = (Property) s.getStringToSplit();
+        assertThat(p.getScope(), is("MR"));
+        assertThat(p.getPath(), is("medication.reference.value"));
+        // assertThat(s.getSeparator(), is("/"));
         assertThat(a.getOperand().get(1), instanceOf(InValueSet.class));
         InValueSet ivs = (InValueSet) a.getOperand().get(1);
         assertThat(ivs.getValueset().getName(), is("Antithrombotic Therapy"));
+        assertThat(ivs.getCode(), instanceOf(FunctionRef.class));
+        FunctionRef fr = (FunctionRef) ivs.getCode();
+        assertThat(fr.getLibraryName(), is("FHIRHelpers"));
+        assertThat(fr.getName(), is("ToConcept"));
+        assertThat(fr.getOperand().size(), is(1));
+        assertThat(fr.getOperand().get(0), instanceOf(Property.class));
+        p = (Property) fr.getOperand().get(0);
+        assertThat(p.getScope(), is("M"));
+        assertThat(p.getPath(), is("code"));
     }
 
     @Test

Src/java/cql-to-elm/src/test/resources/org/cqframework/cql/cql2elm/fhir/r401/TestMedicationRequest.cql

@@ -0,0 +1,15 @@
+library TestMedicationRequest
+
+using FHIR version '4.0.1'
+
+include FHIRHelpers version '4.0.1'
+
+valueset "Antithrombotic Therapy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1110.62'
+
+context Patient
+
+define "Antithrombotic Therapy at Discharge":
+  ["MedicationRequest": medication in "Antithrombotic Therapy"] Antithrombotic
+
+define "Antithrombotic Therapy at Discharge (2)":
+  ["MedicationRequest": "Antithrombotic Therapy"]

Src/java/elm-fhir/src/test/resources/org/cqframework/cql/elm/requirements/fhir/CMS645/CMS645-ModuleDefinitionLibrary.json

@@ -45,17 +45,21 @@
         "valueString": "G10002"
       }, {
         "url": "targetProperty",
-        "valueString": "medication"
+        "valueString": "medication.reference.value"
       } ]
     } ],
     "type": "Medication",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medication" ],
-    "mustSupport": [ "id" ]
+    "mustSupport": [ "id.value", "code" ],
+    "codeFilter": [ {
+      "path": "code",
+      "valueSet": "tbd"
+    } ]
   }, {
     "id": "G10002",
     "type": "MedicationRequest",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest" ],
-    "mustSupport": [ "medication.reference", "status", "status.value", "intent", "intent.value", "doNotPerform", "doNotPerform.value", "dosageInstruction" ]
+    "mustSupport": [ "medication.reference.value", "status", "status.value", "intent", "intent.value", "doNotPerform", "doNotPerform.value", "dosageInstruction" ]
   }, {
     "type": "MedicationRequest",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest" ],

Src/java/elm-fhir/src/test/resources/org/cqframework/cql/elm/requirements/fhir/PCSBMI/PCSBMI-ModuleDefinitionLibrary.json

@@ -1,6 +1,5 @@
 {
   "resourceType": "Library",
-  "name": "EffectiveDataRequirements",
   "extension": [ {
     "url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
     "valueCoding": {
@@ -30,6 +29,7 @@
       "display": "virtual"
     }
   } ],
+  "name": "EffectiveDataRequirements",
   "status": "active",
   "type": {
     "coding": [ {
@@ -455,11 +455,19 @@
   }, {
     "type": "Medication",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medication" ],
-    "mustSupport": [ "id" ]
+    "mustSupport": [ "id.value", "code" ],
+    "codeFilter": [ {
+      "path": "code",
+      "valueSet": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1561"
+    } ]
   }, {
     "type": "Medication",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medication" ],
-    "mustSupport": [ "id" ]
+    "mustSupport": [ "id.value", "code" ],
+    "codeFilter": [ {
+      "path": "code",
+      "valueSet": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.526.3.1562"
+    } ]
   }, {
     "type": "MedicationRequest",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest" ],
@@ -471,7 +479,7 @@
   }, {
     "type": "MedicationRequest",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest" ],
-    "mustSupport": [ "medication.reference" ]
+    "mustSupport": [ "medication.reference.value" ]
   }, {
     "type": "MedicationRequest",
     "profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest" ],